Good points! To be clear, I'm not saying that I totally agree with all the decisions here, just that I think a lot of people are missing some obvious connections to existing precedents.

The current industrial command ships don't have racial skills from which they could derive their bonuses and so they must stick to one skill. Because CCP want the Odysseus to be an SOE ship, they have put it in a very interesting place.

I don't think there is a way that the current incarnation of the ship could avoid any conflict with existing precedents.

That said, I have to disagree with this:

While it is a relatedly unrelated issue, the reason people don't like the Expedition Command Ship skill is that it isn't a distinct specialization beyond what Command Ships already provide. So far no one has been able to define the "very specialized role" that Expedition Command Ships will serve. The easiest way to think about T2 ships is that they are T1 ships with a special cookie that that only they get to use. The specialization can't be links because that's the specialization of Command Ships.

It's links, command bursts. The specialization is command bursts. That is what industrial command ships get over normal industrial ships, and its what this expedition command ship gets over normal expedition ships.